Mutagenesis and comparative sequence analysis of a base triple joining the two domains of group I ribozymes

RNA

Volumn 3, Issue 9, 1997, Pages 1037-1051

  Tanner, Michael A ^a,b   Anderson, Emily M ^a   Gutell, Robin R ^a   Cech, Thomas R ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Anabaena; Azoarcus; RNA structure; Self splicing; Tertiary Interaction; Tetrahymena

Indexed keywords

RIBOZYME;

ANABAENA; ARTICLE; BASE PAIRING; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; RNA CONFORMATION; RNA SEQUENCE; RNA SPLICING; TETRAHYMENA THERMOPHILA;

ANABAENA; ANIMALS; BASE COMPOSITION; BINDING SITES; GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS; HYDROGEN BONDING; INTRONS; MODELS, MOLECULAR; MUTAGENESIS; MUTATION; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA PRECURSORS; RNA, CATALYTIC; SEQUENCE ANALYSIS, DNA; TETRAHYMENA;

ANABAENA; AZOARCUS; EUKARYOTA; TETRAHYMENA; TETRAHYMENA THERMOPHILA;

EID: 0030866522     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (52)

1. Beaudry AA, Joyce GF. 1990. Minimum secondary structure requirements for catalytic activity of a self-splicing group I intron. Biochemistry 29:6534-6539.
2. Been MD, Cech TR. 1986. One binding site determines sequence specificity of Tetrahyrnena pre-rRNA self-splicing, trans-splicing, and RNA enzyme activity. Cell 47:207-216.
3. Been MD, Cech TR. 1987. Selection of circularization sites in a group I IVS RNA requires multiple alignments of an internal template-like sequence. Cell 50:951-961.
4. Been MD, Perrotta AT. 1991. Group I intron self-splicing with adenosine: Evidence for a single nucleotide-binding site. Science 252:434-437.
5. Belfort M, Reaban ME, Coetzee T, Dalgaard JZ. 1995. Prokaryotic introns and inteins: A panoply of form and function. J Bacterial 277:3897-3903.
6. Bevilacqua PC, Kierzek R, Johnson KA, Turner DH. 1992. Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods. Science 258:1355-1358.
7. Burke JM. 1988. Molecular genetics of group I introns: RNA structure and protein factors required for splicing - A review. Gene 73:273-294.
8. Burke JM, Belfort M, Cech TR, Davies RW, Schweyen RJ, Shub DA, Szostak JW, Tabak HF. 1987. Structural conventions for group I introns. Nucleic Acids Res 25:7217-7221.
9. Burke JM, Irvine KD, Kaneko KJ, Kerker BJ, Oettgen AB, Tierney WM, Williamson CL, Zaug AJ, Cech TR. 1986. Role of conserved sequence elements 9L and 2 in self-splicing of the Tetrahymena ribosomal RNA precursor. Cell 45:167-176.
10. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA. 1996. Crystal structure of a group 1 ribozyme domain: Principles of RNA packing. Science 273:1678-1685.
11. Cech TR. 1988. Conserved sequences and structures of group I introns: Building an active site for RNA catalysis - A review. Gene 73:259-271.
12. Cech TR. 1993. Structure and mechanism of the large catalytic RNAs: Group I and group II introns and ribonuclease P. In: Gesteland RF, Atkins JF, eds. The RNA world. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, pp 239-269.
13. Cech TR, Damberger SH, Gutell RR. 1994. Representation of the secondary and tertiary structure of group I introns. Nature Struct Biol 2:273-280.
14. Christian EL, Yarus M. 1993. Metal coordination sites that contribute to structure and catalysis in the group I intron from Tetrahymena. Biochemistry 32:4475-4480.
15. Damberger SH, Gutell RR. 1994. A comparative database of group I intron structures. Nucleic Acids Res 22:3508-3510.
16. Davanloo P, Rosenberg AH, Dunn JJ, Studier FW. 1984. Cloning and expression of the gene for bacteriophage T7 RNA polymerase. Proc Natl Acad Sci USA 81:2035-2039.
17. Davies RW, Waring RB, Ray JA, Brown TA, Scazzocchio C. 1982. Making ends meet: A model for RNA splicing in fungal mitochondria. Nature 300:719-724.
18. Doherty EA, Doudna JA. 1997. The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core. Biochemistry 36:3159-3169.
19. Doudna JA, Cech TR. 1995. Self-assembly of a group I intron active site from its component tertiary structural domains. RNA 1:36-45.
20. Flor PJ, Flanegan JB, Cech TR. 1989. A conserved base pair within helix P4 of the Tetrahymena ribozyme helps to form the tertiary structure required for self-splicing. EMBO J. 11:3391-3399.
21. Gautheret D, Damberger SH, Gutell RR. 1995. Identification of base-triples in RNA using comparative sequence analysis. J. Mol Biol 248:27-43.
22. Golden BL, Cech TR. 1996. Conformational switches involved in orchestrating the successive steps of group I RNA splicing. Biochemistry 35:3754-3763.
23. Gutell RR, Power A, Hertz GZ, Putz IM, Stormo GD. 1992. Identifying constraints on the higher-order structure of RNA: Continued development and application of comparative sequence analysis methods. Nucleic Acids Res 20:5785-5795.
24. Herschlag D. 1992. Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme. Biochemistry 33:1386-1399.
25. Inoue T, Cech TR. 1985. Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: A technique for RNA structure analysis using chemical probes and reverse transcriptase. Proc Natl Acad Sci USA 82:648-652.
26. Jaeger L, Michel F, Westhof E. 1994. Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J. Mol Biol 236:1271-1276.
27. Jaeger L, Michel F, Westhof E. 1996. The structure of group I ribozymes. In: Eckstein F, Lilley DMJ, eds. Nucleic acids and molecular biology, vol 10. Berlin/Heidelberg: Springer-Verlag, pp 33-51.
28. Kim SH, Quigley GJ, Suddath FL, McPherson A, Sneden D, Kim JJ, Weinzierl J, Rich A. 1973. Three-dimensional structure of yeast phenylalanine transfer RNA: Folding of the polynucleotide chain. Science 179:285-288.
29. Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR. 1982. Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31:147-157.
30. Laggerbauer B, Murphy FL, Cech TR. 1994. Two major tertiary folding transitions of the Tetrahymena catalytic RNA. EMBO J. 33:2669-2676.
31. Lambowitz AM, Perlman PS. 1990. Involvement of aminoacyl-tRNA synthetases and other proteins in group I and group II intron splicing. Trends Biochem Sci 35:440-444.
32. Lehnert V, Jaeger L, Michel F, Westhof E. 1996. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: A complete 3D model of the Tetrahymena thermophila ribozyme. Chem & Biol 3:993-1009.
33. Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ, Woese CR. 1996. The Ribosomal Database Project (RDB). Nucleic Acids Res 24:82-85.
34. Michel F, Ellington AD, Couture S, Szostak JW. 1990. Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns. Nature 347:578-580.
35. Michel F, Hanna M, Green R, Bartel DP, Szostak JW. 1989. The guanosine binding site of the Tetrahymena ribozyme. Nature 342:391-395.
36. Michel F, Jacquier A, Dujon B. 1982. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie 64:867-881.
37. Michel F, Jaeger L, Westhof E, Kuras R, Tihy F, Xu MQ, Shub DA. 1992. Activation of the catalytic core of a group 1 intron by a remote 3' splice junction. Genes & Dev 6:1373-1385.
38. Michel F, Westhof E. 1990. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol Biol 226:585-610.
39. Murphy FL, Cech TR. 1994. GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain. J. Mol Biol 236:49-63.
40. Pley HW, Flaherty KM, McKay DB. 1994. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature 372:111-113.
41. Reinhold-Hurek B, Shub DA. 1992. Self-splicing introns in tRNA genes of widely divergent bacteria. Nature 357:173-176.
42. Robertus JD, Ladner JE, Finch JT, Rhodes D, Brown RS, Clark BF, Klug A. 1974. Structure of yeast phenylalam'ne tRNA at 3 A resolution. Nature 250:546-551.
43. Streicher B, Westhof E, Schroeder R. 1996. The environment of two metal ions surrounding the splice site of a group I intron. EMBO J 15:2556-2564.
44. Strobel SA, Shetty K. 1997. Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping. Proc Natl Acad Sci USA 94:2903-2908.
45. IIe of the purple bacterium Azoarcus. RNA 2:74-83.
46. Tanner MA, Cech TR. 1997. Joining the two domains of a group I ribozyme to form the catalytic core. Science 275:847-849.
47. Wang JF, Downs WD, Cech TR. 1993. Movement of the guide sequence during RNA catalysis by a group I ribozyme. Science 260:504-508.
48. Waring RB. 1989. Identification of phosphate groups important to self-splicing of the Tetrahymena rRNA intron as determined by phosphorothioate substitution. Nucleic Acids Res 27:10281-10293.
49. Waring RB, Scazzocchio C, Brown TA, Davies RW. 1983. Close relationship between certain nuclear and mitochondrial introns: Implication for the mechanism of RN A splicing. J Mol Biol 267:595-605.
50. Xu MQ, Kathe SD, Goodrich-Blair H, Nierzwicki-Bauer SA, Shub DA. 1990. Bacterial origin of a chloroplast intron: Conserved self-splicing group I introns in cyanobacteria. Science 250:1566-1570.
51. Zaug AJ, Grabowski PJ, Cech TR. 1983. Autocatalytic cyclization of an excised intervening sequence RNA is a cleavage-ligation reaction. Nature 302:578-583.
52. Zaug AJ, McEvoy MM, Cech TR. 1993. Self-splicing of the group I intron from Anabaena pre-tRNA: Requirement for base-pairing of the exons in the anticodon stem. Biochemistry 32:7946-7953.